A package structure is provided. The package structure includes a through substrate via structure, a first stacked die package structure, an underfill layer, and a package layer. The through substrate via structure is formed over a substrate. The first stacked die package structure is over the through substrate via structure, wherein the first stacked die package structure comprises a plurality of memory dies. The underfill layer is over the first stacked die package structure. the package layer is over the underfill layer, wherein the package layer has a protruding portion that extends below a top surface of the through substrate via structure.